1. I am able to reproduce the problem with perspective and masks. But not in every case. What works is: apply guided perspective and then add a mask. Adding a mask first and then perspective (which is a bit unusual IMO) will shift. Also, the vertical / horizontal sliders appear to mess up the mask too. Thanks for reporting the bug.
2. I don’t know about #2 – it could be a situation when the app is simply confused.
3. Rotating can be slow if the window is large. You can use the straighten tool to avoid this problem.
4. Guided Perspective already allows you to zoom in. While I can imagine transparent or thinner lines might help, they may be invisible in certain images. When I have made the lines thinner in the past, people ask for thicker ones. When they are thicker, people want them thinner. /shrug